Re: [spctools-discuss] Re: Libra quantification

2017-03-02 Thread Jimmy Eng 
Chris, it should work with your mzXML file just as well.  If it's failing,
it's for another reason.  As I mentioned in the comet-ms google group, I
can follow-up with you offline to figure out what's not working for you.

On Thu, Mar 2, 2017 at 6:04 PM, Chris Barnes 
wrote:

> Hi Jimmy,
>
> I don't know if this will still be updated, but I did exactly what you say
> above and still got this same error.  The only difference is that I had the
> Thermo raw files that I converted to mzXML.  Does it only work if I convert
> to mzML for some reason?  I actually just tried it again on a test file
> converted to mzML and I was able to get an output for the quantitation
> table, so maybe the mzXML/mzML is the difference?  Is that possible?
>
> Best,
>
> chris
>
>
>
>
>
>
> On Wednesday, October 28, 2015 at 6:49:06 PM UTC-7, Jimmy Eng wrote:
>>
>> Actually for both of you, your best bet is to start with the mzML file
>> that you generate from your mgf using msconvert.  Search that with your
>> search tool of choice and then run Libra.  That should work.
>>
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Re: [spctools-discuss] Re: Libra quantification

2017-03-02 Thread Chris Barnes 
Hi Jimmy,

I don't know if this will still be updated, but I did exactly what you say 
above and still got this same error.  The only difference is that I had the 
Thermo raw files that I converted to mzXML.  Does it only work if I convert 
to mzML for some reason?  I actually just tried it again on a test file 
converted to mzML and I was able to get an output for the quantitation 
table, so maybe the mzXML/mzML is the difference?  Is that possible?

Best,

chris






On Wednesday, October 28, 2015 at 6:49:06 PM UTC-7, Jimmy Eng wrote:
>
> Actually for both of you, your best bet is to start with the mzML file 
> that you generate from your mgf using msconvert.  Search that with your 
> search tool of choice and then run Libra.  That should work.
>

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Re: [spctools-discuss] Re: Libra quantification

2015-10-28 Thread Jimmy Eng 
The problem is due to starting out with the mgf file.  Libra and the TPP
tools needs to know which spectrum/scan in the mgf/mzML file is associated
with which identification.  So there needs to be some type of convention in
how the mgf file annotates this which means you can't start with just any
mgf file.  That mgf file needs to be produced by the TPP tools or with
msconvert such that the TITLE line for each spectrum is of the format:

   TITLE=...
e.g.
   TITLE=JE102306.00594.00594.2

If you have your mgf in this file, tools such as Comet will/should annotate
that scan as scan 594 in the "spectrum_query" element of the pep.xml file.
Libra will then know to read scan 594 of the corresponding mzML/mzXML file
to pull out the iTRAQ/TMT peaks.

Again, if you start out with an mzML file, you can generate the mgf using
the TPP tools and it will have the correct format.  You can also start out
with a raw file or mzML and use msconvert with the following titleMaker
option to accomplish the same thing:
--filter "titleMaker ...
There's no easy fix that I'm aware of if you start with a random mgf file
that does not have TITLE lines that conform to this convention.

- Jimmy

On Wed, Oct 28, 2015 at 5:13 PM, zeyu sun  wrote:

> Hi, Henry,
> I have the same problem. I use the the Comet to do the search, and when I
> use Libra function in peptide analysis module, I got this message:
>
>  Error ms2 filter line:
>
> I don't really know what causes this, anyone in TPP team know how to solve 
> this?
>
>
> SunSun
>
>
>
> On Sunday, March 29, 2015 at 8:10:34 AM UTC+8, Henry Rodríguez wrote:
>>
>> Hi,
>>
>> I am performing a quantification of my data with Libra software. However,
>> I always obtain a error. My original spectra are in *MGF format*, so I
>> convert them to mzML with MSConvert software of Proteowizard with different
>> filters, but this does not functioned. Also, I have tried use the
>> ScanRanker software which filter for quality the spectra (
>> http://fenchurch.mc.vanderbilt.edu/bumbershoot/scanranker/index.html),
>> but this also does not functioned. The error that I have obtained is the
>> following. Thanks for your help with this error,
>>
>> Henry.
>>
>>
>>
>> Analyzing interact_rawdata280315.pep.xml ...
>> Parsing search results 
>> "c:/Inetpub/wwwroot/ISB/data/Rawdata_Peakpicking2/PAIV141024_1 (X! Tandem 
>> (k-score))"...
>>   => Found 34 hits. (0 decoys, 0 excluded)
>>   => Total so far: 34 hits. (0 decoys, 0 excluded)
>> Parsing search results 
>> "c:/Inetpub/wwwroot/ISB/data/Rawdata_Peakpicking2/PAIV141024_2 (X! Tandem 
>> (k-score))"...
>>   => Found 68 hits. (0 decoys, 0 excluded)
>>   => Total so far: 102 hits. (0 decoys, 0 excluded)
>> El sistema no puede encontrar la ruta especificada.
>> command completed in 1 sec
>>
>> running: "C:/Inetpub/tpp-bin/LibraPeptideParser 
>> "interact_rawdata280315.pep.xml" -ccondition.xml"
>>  Error ms2 filter line:
>>
>>
>> command "C:/Inetpub/tpp-bin/LibraPeptideParser 
>> "interact_rawdata280315.pep.xml" -ccondition.xml" failed: Operation not 
>> permitted
>>
>> command "C:/Inetpub/tpp-bin/LibraPeptideParser 
>> "interact_rawdata280315.pep.xml" -ccondition.xml" exited with non-zero exit 
>> code: 1
>> QUIT - the job is incomplete
>>
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Re: [spctools-discuss] Re: Libra quantification

2015-10-28 Thread Jimmy Eng 
Actually for both of you, your best bet is to start with the mzML file that
you generate from your mgf using msconvert.  Search that with your search
tool of choice and then run Libra.  That should work.

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